Although being great tools, Munin and other RRDTool frontends (such as Cacti or Ganglia) have known i/o issues and are dificcult to scale when you monitor hundreads of nodes.
There are some techniques to deal with this i/o bottleneck though. One of these thecniques is to spread writes across a large number of disks to reduce i/o in each disk. On the other hand, many sysadmins use tmpfs filesystems to deal with this problem. RRDCached is also a recent and good option to deal with this and I'd recommend you take a look at this slides.
I'm not that familiar with Munin, but Cacti has a Boost plugin. This plugin caches data in memory and performs mass and on-demand updates to disk, instead of individual writes, thus reducing i/o. I'm pretty sure that Munin has also something like this.
If you can afford them, SSD disks are also good options.
Last but not least, you can also take a look at Reconnoiter. Recconoiter is a brand new fault detection and graphing/trending tool. Unlike most trending tools, Reconnoiter is not RRDTool based and tries to solve this specific issue. I'm not using Reconnoiter in production, but I've made some tests, and despite still being a little "green", looks really promising, especially regarding its scalability.
Hope this helps!